Wow, there is a lot of logic in this discussion. For me, when i first played through ME1, without refering to a walkthrough, or seeing any spoilers, it was one of those tough choices. what made it worst was my having Ashley and Liara on my sqaud. Both had differing opinions, but I thought of it this way:
During the Rachni wars, the Rachni fought the council without mercy. They were so vicious, that the council had to find the second most vicious race, the Krogan. The Council armed a potential threat to deal with what they couldn't deal with. Why? Because the Rachni never comunicated with the council. To the council, the Rachni were a race of savage murderers, partly because they are, secondly because the Rachni were isolated and didn't know how to communicate with outsiders. For all we know, they probably thought the council were the savages. This Queen is inheritedly different because she was Hatched by "outsiders", she observed them, and learned how they communicated. She lost any preconception of outsiders being completely savage due to her time spent with them. Thus she learned that it was better to communicate before starting aggression. Learning this shows that above all, the Rachni are capable of changing. Whether or not they do is up to the queen, but its been shown that they aren't hostile anymore. This is proven more by your encounter in ME2. The Rachni could had killed the Asari, as their brutal nature implied, but they saved her and fixed her ship.
Anyway, as they say in England "God save the Queen"